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I have just finished a pc build with a SSD to be used as the boot/OS drive and a secondary 2 HDD setup in raid 0 for storage.

First I started with the SSD only and installed win7, applied all the updates etc. At this point the system has rebooted at least half a dozen times with no issue.
Next I set up the 2 HDD in raid 0, initialized it with disk manager and everything is looking good. But as soon as I reboot the system, upon startup the system can't find a os. Using the windows install disc, I go into the recovery console and discover that the boot drive which was C:\ is now E:\ and the storage drive which was E:\ is now C:\.
The os files on the boot drive seem to be all there. It's just in the wrong drive path. Using the recovery console I switched back the drives to their proper places, but then on startup I got the error 'bootmgr is missing' at this point I gave up, nuked the drives and started from scratch only to get thing again once I initialized the HDD and rebooted.
I am sure I have overlooked some stupid detail somewhere. Can anyone help me figure out where I went wrong?

I have checked the bios settings over and over and I confidant that the bios setting are good. The drives don't disappear, they just change pecking order. I noticed on my last loadup that in disk manager the HDD array is marked as volume 0, and the SSD is marked as volume 1. Is it possible that once I initialize the HDD array it takes priority due to it being volume 0, thus becoming C:\ and bumping the SSD marked as volume 1 to E:\. Maybe I need to have the HDD array physically disconnected from the motherboard, and not just connected but in a unformatted state. Opinions?

First no the all the drives were connected when I did the install. The HDD were in a fresh unformatted state. Second I can't change the sata port of the SSD, it's a Crucial 128gb sata m.2 attached directly to the motherboard.None of the drives had a partition of any sort except the 100mb made by the windows install on the SSD. And third I made sure over and over again that the boot sequence was only the SSD, I even erased the raid array but it made no difference. The more I think of it, I think the error I made was having all the drives connected, instead of only the SSD physically connected loading windows then physically connect the HDD array.

No there was no 100mb partition on the HDD array.
I am going to disconnect the HDD array and reinstall windows, then connect the HDD and see what happens. Hopefully this will do the trick. I let you guys know how it goes later on tonight.
Thanks a lot to everyone for the helping hand

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